Changed name to CompAIRR and version to 0.1.0

uio-bmi · May 25, 2021 · 2261c53 · 2261c53
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diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
-# vdjsearch
+# CompAIRR
 
-The command line tool `vdjsearch` can be used to compare two sets of
-immune receptor repertoires. It can also be used to cluster the
-sequences in a repertoire.
+CompAIRR (`compairr`) is a command line tool to compare two sets of
+immune receptor repertoires, or cluster the sequences in one
+repertoire.
 
 
 ## General options
@@ -107,9 +107,9 @@ input.
 ## Command line options
 
 ```
-vdjsearch 0.0.4 - Immune repertoire analysis
+CompAIRR 0.1.0 - Compare Adaptive Immune Receptor Repertoires
 
-Usage: vdjsearch [OPTIONS] TSVFILE1 [TSVFILE2]
+Usage: compairr [OPTIONS] TSVFILE1 [TSVFILE2]
 
 Commands:
  -h, --help                  display this help and exit
@@ -150,12 +150,12 @@ CASSTSHQQYF	0.07	TCRBV07-06	TCRBJ02-01	B2
 
 We run the following command:
 
-`vdjsearch -m -d 1 -o output.tsv seta.tsv setb.tsv`
+`compairr -m -d 1 -o output.tsv seta.tsv setb.tsv`
 
 Here is the output to the console:
 
 ```
-vdjsearch 0.0.4 - Immune repertoire analysis
+CompAIRR 0.1.0 - Immune repertoire analysis
 
 Command:           Overlap
 Repertoire set 1:  seta.tsv
@@ -265,7 +265,7 @@ As a preliminary performance test, Cohort 2 ("Keck") of
 [the dataset](https://s3-us-west-2.amazonaws.com/publishedproject-supplements/emerson-2017-natgen/emerson-2017-natgen.zip)
 by Emerson et al. was compared to itself. It contains 120 repertoires
 with a total of 24 544 336 sequences. The test was performed with
-vdjsearch version 0.0.3. The timing results are shown below.
+version 0.0.3 of the tool. The timing results are shown below.
 
 Distance | Indels | Threads | Time (s) | Time (mm:ss)
 -------: | :----: | ------: | -------: | -----------:

diff --git a/src/Makefile b/src/Makefile
@@ -17,7 +17,7 @@
 #    Department of Informatics, University of Oslo,
 #    PO Box 1080 Blindern, NO-0316 Oslo, Norway
 
-# Makefile for vdjsearch
+# Makefile for CompAIRR
 
 COMMON = -g -std=c++11
 EXTRAOBJ =
@@ -69,24 +69,24 @@ LINKFLAGS = $(COMMON) $(LINKOPT)
 
 CXXFLAGS = $(COMMON) $(WARNINGS)
 
-PROG = vdjsearch
+PROG = compairr
 
-OBJS = arch.o bloompat.o cluster.o db.o hashtable.o overlap.o \
-	util.o variants.o vdjsearch.o zobrist.o
+OBJS = arch.o bloompat.o cluster.o compairr.o db.o hashtable.o \
+	overlap.o util.o variants.o zobrist.o
 
 DEPS = Makefile threads.h \
-	arch.h bloompat.h cluster.h db.h hashtable.h overlap.h \
-	util.h variants.h vdjsearch.h zobrist.h
+	arch.h bloompat.h cluster.h compairr.h db.h hashtable.h \
+	overlap.h util.h variants.h zobrist.h
 
 all : $(PROG)
 
-vdjsearch : $(OBJS) $(DEPS)
+compairr : $(OBJS) $(DEPS)
 	$(CXX) $(LINKFLAGS) -o $@ $(OBJS) $(LIBS)
 	mkdir -p ../bin
-	cp -a vdjsearch ../bin
+	cp -a compairr ../bin
 
 clean :
-	rm -rf vdjsearch *.o *~ gmon.out *.gcno *.gcda *.gcov
+	rm -rf compairr *.o *~ gmon.out *.gcno *.gcda *.gcov
 
 .o : .cc $(DEPS)
 	$(CXX) $(CXXFLAGS) -c -o $@ $<
diff --git a/src/arch.cc b/src/arch.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 uint64_t arch_get_memused()
 {

diff --git a/src/bloompat.cc b/src/bloompat.cc
@@ -29,7 +29,7 @@
   https://doi.org/10.1145/1498698.1594230
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 void bloom_patterns_generate(struct bloom_s * b);
 

diff --git a/src/cluster.cc b/src/cluster.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 const unsigned int no_cluster = UINT_MAX;
 

diff --git a/src/vdjsearch.cc → src/compairr.cc b/src/vdjsearch.cc → src/compairr.cc
@@ -38,7 +38,7 @@
 
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 /* OPTIONS */
 

diff --git a/src/vdjsearch.h → src/compairr.h b/src/vdjsearch.h → src/compairr.h
@@ -95,9 +95,9 @@ static_assert(INT_MAX > 32767, "Your compiler uses very short integers.");
 
 /* constants */
 
-#define PROG_CMD "vdjsearch"
-#define PROG_NAME "VDJsearch"
-#define PROG_VERSION "0.0.5"
+#define PROG_CMD "compairr"
+#define PROG_NAME "CompAIRR"
+#define PROG_VERSION "0.1.0"
 #define PROG_BRIEF "Compare Adaptive Immune Receptor Repertoires"
 
 const unsigned int MAX_THREADS = 256;

diff --git a/src/db.cc b/src/db.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 /* How much memory for residues and sequences should we allocate each time? */
 

diff --git a/src/hashtable.cc b/src/hashtable.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 #define HASHFILLPCT 70
 

diff --git a/src/overlap.cc b/src/overlap.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 static struct db * d;
 static unsigned int set1_longestsequence = 0;

diff --git a/src/util.cc b/src/util.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 static const char * progress_prompt;
 static uint64_t progress_next;

diff --git a/src/variants.cc b/src/variants.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 //#define DUMP 1
 #define SMART 1

diff --git a/src/zobrist.cc b/src/zobrist.cc
@@ -19,7 +19,7 @@
     PO Box 1080 Blindern, NO-0316 Oslo, Norway
 */
 
-#include "vdjsearch.h"
+#include "compairr.h"
 
 uint64_t * zobrist_tab_base = nullptr;
 static uint64_t * zobrist_v_base = nullptr;